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- PDB-1xi8: Molybdenum cofactor biosynthesis protein from Pyrococcus furiosus... -

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Basic information

Entry
Database: PDB / ID: 1xi8
TitleMolybdenum cofactor biosynthesis protein from Pyrococcus furiosus Pfu-1657500-001
ComponentsMolybdenum cofactor biosynthesis protein
KeywordsStructural genomics / unknown function / Molybdenum cofactor biosynthesis protein / Pyrococcus furiosus / Southeast Collaboratory for Structural Genomics / hyperthermophile / PSI / Protein Structure Initiative / SECSG
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process
Similarity search - Function
Beta-clip / MoeA, C-terminal, domain IV / Molybdopterin biosynthesis moea protein, domain 2 / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) ...Beta-clip / MoeA, C-terminal, domain IV / Molybdopterin biosynthesis moea protein, domain 2 / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdopterin biosynthesis moea protein, domain 2 / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Molybdenum cofactor biosynthesis protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.504 Å
AuthorsZhou, W. / Zhao, M. / Chang, J.C. / Liu, Z.-J. / Chen, L. / Horanyi, P. / Xu, H. / Yang, H. / Habel, J.E. / Lee, D. ...Zhou, W. / Zhao, M. / Chang, J.C. / Liu, Z.-J. / Chen, L. / Horanyi, P. / Xu, H. / Yang, H. / Habel, J.E. / Lee, D. / Chang, S.-H. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Molybdenum cofactor biosynthesis protein from Pyrococcus furiosus Pfu-1657500-001
Authors: Zhou, W. / Zhao, M. / Chang, J.C. / Liu, Z.-J. / Chen, L. / Horanyi, P. / Xu, H. / Yang, H. / Habel, J.E. / Lee, D. / Chang, S.-H. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics
History
DepositionSep 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein
B: Molybdenum cofactor biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)89,5992
Polymers89,5992
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-30 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.547, 116.599, 147.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsnot known

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Components

#1: Protein Molybdenum cofactor biosynthesis protein


Mass: 44799.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET24d Bam / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star DE3 pRIL / References: UniProt: Q8U034

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 291 K / Method: modified microbatch
Details: 25.5%w/v PEG-8000, 0.17M ammonium sulfate, 15%v/v glycerol, pH no buffer, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 37143 / % possible obs: 96.6 % / Rmerge(I) obs: 0.051 / Χ2: 0.964
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2% possible all
2.5-2.590.31630500.76781.2
2.59-2.690.28133921.01589.8
2.69-2.820.21236420.77495.8
2.82-2.960.19437700.79599.5
2.96-3.150.12438120.858100
3.15-3.390.0838080.961100
3.39-3.730.06238451.267100
3.73-4.270.0438551.088100
4.27-5.380.02939070.975100
5.38-500.02540621.01599.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1FC5

1fc5


Resolution: 2.504→42.954 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.847 / WRfactor Rfree: 0.326 / WRfactor Rwork: 0.3 / SU B: 12.319 / SU ML: 0.271 / SU R Cruickshank DPI: 0.363 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.3
RfactorNum. reflection% reflectionSelection details
Rfree0.343 1875 5.067 %thin shells
Rwork0.306 ---
all0.308 ---
obs-37001 96.199 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 52.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.018 Å20 Å20 Å2
2--0.038 Å20 Å2
3----0.021 Å2
Refinement stepCycle: LAST / Resolution: 2.504→42.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 0 0 4034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224092
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9955564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9635524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75124.286154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51515665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2711519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023002
X-RAY DIFFRACTIONr_nbd_refined0.2440.31787
X-RAY DIFFRACTIONr_nbtor_refined0.3280.52816
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.5204
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.320
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3180.51
X-RAY DIFFRACTIONr_mcbond_it01.52698
X-RAY DIFFRACTIONr_mcangle_it024236
X-RAY DIFFRACTIONr_scbond_it031565
X-RAY DIFFRACTIONr_scangle_it04.51328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.504-2.5680.4721250.4242039277378.038
2.568-2.6390.5021250.412213273485.516
2.639-2.7150.4351250.3822308264591.985
2.715-2.7980.4111250.3482329257295.412
2.798-2.8890.391250.3462370252099.008
2.889-2.990.3621250.3452279240599.958
2.99-3.1030.341250.3222224235099.957
3.103-3.2290.4051250.3452119224699.911
3.229-3.3710.3561250.3312049217599.954
3.371-3.53500.3272063209698.426
3.535-3.7250.3661250.3121840197799.393
3.725-3.9490.3071250.281725186399.302
3.949-4.2190.2941250.2591660179899.277
4.219-4.55300.2321654165599.94
4.553-4.9820.2311250.23213961521100
4.982-5.5610.351690.27813471416100
5.561-6.4030.365560.32111931249100
6.403-7.79900.33910731073100
7.799-10.8520.3711250.26472985799.65
10.852-42.95400.41951653895.911

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